CENATAC

centrosomal AT-AC splicing factor

Basic information

Region (hg38): 11:118998138-119015793

Previous symbols: [ "CCDC84" ]

Links

ENSG00000186166 ∙ NCBI:338657 ∙ OMIM:620142 ∙ HGNC:30460 ∙ Uniprot:Q86UT8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mosaic variegated aneuploidy syndrome 4 (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CENATAC gene.

• not_specified (63 variants)
• Mosaic_variegated_aneuploidy_syndrome_4 (3 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENATAC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198489.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense	1		60	4		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1					1
Total	2	0	60	4	0

Highest pathogenic variant AF is 0.000011240431

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENATAC	protein_coding	protein_coding	ENST00000334418	11	17650

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.47e-14	0.0543	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0494	186	188	0.990	0.00000928	2158
Missense in Polyphen		79	79.839	0.98949		874
Synonymous	1.18	53	65.1	0.814	0.00000286	599
Loss of Function	0.502	22	24.7	0.891	0.00000127	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00115
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000395	0.000387
Middle Eastern	0.000218	0.000217
South Asian	0.000269	0.000261
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.847
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.0974
• hipred: N
• hipred_score: 0.167
• ghis: 0.590

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccdc84